Mercurial > repos > greg > vsnp_statistics
changeset 18:076069733de7 draft
Uploaded
| author | greg |
|---|---|
| date | Wed, 04 Aug 2021 13:27:17 +0000 |
| parents | 932e517b5779 |
| children | ae006e01b0fa |
| files | .shed.yml test-data/vsnp_statistics4.tabular vsnp_statistics.xml |
| diffstat | 3 files changed, 17 insertions(+), 3 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Wed Aug 04 13:27:17 2021 +0000 @@ -0,0 +1,13 @@ +name: vsnp_statistics +owner: greg +description: | + Contains a tool that produces an Excel spreadsheet containing statistics for samples and associated metrics files. +homepage_url: https://github.com/USDA-VS/vSNP +long_description: | + Contains a tool Accepts a single fastqsanger sample, a set of paired read samples, or a collections of samples + along with associated SAMtools idxstats and vSNP zero coverage metrics files and extracts information from them + to produce an Excel spreadsheet containing statistics for each sample. +remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_statistics +type: unrestricted +categories: + - Sequence Analysis
--- a/test-data/vsnp_statistics4.tabular Tue Aug 03 19:52:56 2021 +0000 +++ b/test-data/vsnp_statistics4.tabular Wed Aug 04 13:27:17 2021 +0000 @@ -1,2 +1,2 @@ Reference Read1 FASTQ File Size Reads Mean Read Length Mean Read Quality Reads Passing Q30 Read2 FASTQ File Size Reads Mean Read Length Mean Read Quality Reads Passing Q30 Total Reads All Mapped Reads Unmapped Reads Unmapped Reads Percentage of Total Reference with Coverage Average Depth of Coverage Good SNP Count -89 forward 8.7 KB 25 100.0 65.7 1.00 reverse 8.5 KB 25 100.0 66.3 1.00 50 46 4 0.08 0.16% 0.002146 0 +89 Unnamed Collection_R1 8.7 KB 25 100.0 65.7 1.00 Unnamed Collection_R2 8.5 KB 25 100.0 66.3 1.00 50 46 4 0.08 0.16% 0.002146 0
--- a/vsnp_statistics.xml Tue Aug 03 19:52:56 2021 +0000 +++ b/vsnp_statistics.xml Wed Aug 04 13:27:17 2021 +0000 @@ -23,11 +23,12 @@ ln -s '${read2}' '${read2_identifier}' && #end if #else: + #set identifier = re.sub('[^\s\w\-]', '_', str($input_type_cond.reads_collection.element_identifier)) #set read1 = $input_type_cond.reads_collection.forward - #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier)) + #set read1_identifier = $identifier + '_R1' ln -s '${read1}' '${read1_identifier}' && #set read2 = $input_type_cond.reads_collection.reverse - #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) + #set read2_identifier = $identifier + '_R2' ln -s '${read2}' '${read2_identifier}' && #end if